Subwavelength structures (SWS), a form of diffractive optic, are well-known for their ability to function as polarizers and anti-reflection coatings. They can also be used to create narrowband optical filters whose surface reflectance spectra exhibit resonant peaks that are highly wavelength dependent, especially as the surface index is modified by the deposition or adsorption of biomaterials such as molecules or cells. In this study, we report on the design and fabrication of SWS structures in silicon that are suitable for use as biosensors in sensitive molecular detection. The structures combine a two-dimensional dielectric grating and Si/SiO2 optical waveguide to create a surface that can function as a narrowband optical filter. The SWS structures were fabricated using a combination of three-beam interference lithography and reactive-ion etching in a CBrF3 plasma. This produced a two-dimensional periodic nanostructure grating array, having a period of ~450 nm and air pores of ~265 nm, within a 300 nm thick silicon layer that serves as the core waveguide region of the filter. The ability to achieve sensitive molecular detection (< nm) is expected by virtue of working with high-index silicon-based structures, but may be practically limited by the need to detect the reflectance at near-infrared, rather than visible, wavelengths.